def createImg(filename, thres=0, samples=1):
count = parseLineage(filename)
suffix, matrix, taxo = getSuffixandMatrixandNewick(count,thres,samples)
newick = convert(taxo,suffix)
newick += ';'
t = Tree(newick, format=1)
ct = ClusterTree(t.write(), text_array=matrix)
addColors(ct)
# nodes are linked to the array table
array = ct.arraytable
# Calculates some stats on the matrix. Needed to establish the color gradients.
matrix_dist = [i for r in xrange(len(array.matrix))for i in array.matrix[r] if np.isfinite(i)]
matrix_max = np.max(matrix_dist)
matrix_min = np.min(matrix_dist)
matrix_avg = (matrix_max+matrix_min)/2
# Creates a profile face that will represent node's profile as a heatmap
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 14, "heatmap",colorscheme=3)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=2
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
# ct.show(tree_style=ts)
filedir = '/'.join(filename.split('/')[:-1])
# t.write(format=9, outfile="output/newick/"+param+".nw")
ct.render(filedir+'/phylo.png',tree_style=ts)
if node.is_leaf():
ColorCode=PhenoDict[node.name]
if ColorCode == '1':
#Name=faces.AttrFace('name',fsize='20',fgcolor="Blue")
#NameFace=TextFace(Name)
faces.add_face_to_node(AttrFace('name',fsize=20,fgcolor='blue'), node, column=0,aligned=True)
#faces.add_face_to_node(TextFace(text='marker1',fsize=10,fgcolor='black'), node, column=1,position='aligned')
faces.add_face_to_node(ProfileFace(1, -1, 0, width=200, height=40, style='heatmap', colorscheme=2),node,column=1,position='aligned')
elif ColorCode == '2':
#Name=faces.AttrFace('name',fsize='20',fgcolor="Red")
#NameFace=TextFace(Name)
faces.add_face_to_node(AttrFace("name",fsize=20,fgcolor='red'), node, column=0,aligned=True)
faces.add_face_to_node(ProfileFace(1, -1, 0, width=200, height=40, style='heatmap', colorscheme=2),node,column=1,position='aligned')
elif ColorCode == '-9':
faces.add_face_to_node(AttrFace("name",fsize=20,fgcolor='black'), node, column=0,aligned=True)
faces.add_face_to_node(ProfileFace(1, -1, 0, width=200, height=40, style='heatmap', colorscheme=2),node,column=1,position='aligned')
ts = TreeStyle()
ts.layout_fn= ColorCodedNode
ts.mode='c' #Circular tree
ts.show_scale = False
ts.show_leaf_name = False
ts.draw_guiding_lines=True
t.render("mytree50.png", w=3840, units="px",tree_style=ts)
def make_cluster_tree(tree_file: str,
matrix: str,
out_file: str,
outgroup: Optional[List[str]] = None) -> None:
"""Draw a tree with cluster absence/presence information from an existing
tree file and absence/presence matrix, and save it as an image under the
supplied file name.
Arguments:
tree_file: the name of the file containing the tree to annotate
matrix: a comma- or tab-separated absence/presence matrix
out_file: the name under which to save the resulting image
outgroup: the organism(s) to use as an outgroup, if any
"""
# ClusterTree needs tab-separated, but that can't be exported cleanly
matrix = matrix.replace(",", "\t")
# tree with clustering analysis
tree = ClusterTree(tree_file, text_array=matrix)
# rerooting the tree
if outgroup:
ancestor = tree.get_common_ancestor(outgroup)
tree.set_outgroup(ancestor)
tree.ladderize(direction=1)
# set drawing line width to 2
my_node_style = NodeStyle()
my_node_style["vt_line_width"] = 2
my_node_style["hz_line_width"] = 2
my_node_style["size"] = 5
# layout function
def sel_mylayout(node):
node.set_style(my_node_style)
if node.is_leaf():
# add names in larger font + italics
species_name = AttrFace("name", fsize=12, fstyle="italic")
add_face_to_node(species_name,
node,
column=0,
position="branch-right")
# add absence/presence matrix
for i, value in enumerate(getattr(node, "profile", [])):
if value > 0:
color = "#FF0000"
else:
color = "#EEEEEE"
my_face = CircleFace(8, color, style="circle")
my_face.margin_right = 3
my_face.margin_bottom = 3
add_face_to_node(my_face, node, position="aligned", column=i)
# Use my layout to visualize the tree
my_tree_style = TreeStyle()
# Add header
for j, name in enumerate(tree.arraytable.colNames):
name_face = TextFace(name, fsize=11)
name_face.rotation = -90
name_face.hz_align = 1
name_face.vt_align = 1
name_face.margin_bottom = 10
my_tree_style.aligned_header.add_face(name_face, column=j)
my_tree_style.scale_length = 0.1
# myTreeStyle.show_branch_support = True
# don't auto-show leaf names, since we dealt with that above
my_tree_style.show_leaf_name = False
# set layout function for my_tree_style
my_tree_style.layout_fn = sel_mylayout
#tree.render(out_file, w=183, units="mm", dpi=600, tree_style=my_tree_style)
tree.render(out_file, dpi=600, tree_style=my_tree_style)
def plot_heat_tree_V0(heatmap_file, tree_file, output_file=None):
'''
Plot heatmap next to a tree. The order of the heatmap **MUST** be the same,
as order of the leafs on the tree. The tree must be in the Newick format. If
*output_file* is specified, then heat-tree will be rendered as a PNG,
otherwise interactive browser will pop-up with your heat-tree.
Parameters
----------
heatmap_file: str
Path to the heatmap file. The first row must have '#Names' as first
element of the header.
e.g. #Names, A, B, C, D
row1, 2, 4, 0, 4
row2, 4, 6, 2, -1
tree_file: str
Path to the tree file in Newick format. The leaf node labels should
be the same as as row names in the heatmap file. E.g. row1, row2.
output_file: str, optional
If specified the heat-tree will be rendered in that file as a PNG image,
otherwise interactive browser will pop-up. **N.B.** program will wait
for you to exit the browser before continuing.
'''
import numpy
from ete3.treeview.faces import add_face_to_node
from ete3 import ClusterTree, TreeStyle, AttrFace, ProfileFace
# To operate with numbers efficiently
# Loads tree and array
t = ClusterTree(tree_file, heatmap_file)
t.ladderize()
R = t.get_midpoint_outgroup()
t.set_outgroup(R)
# nodes are linked to the array table
array = t.arraytable
# Calculates some stats on the matrix. Needed to establish the color
# gradients.
matrix_dist = [i for r in xrange(len(array.matrix))\
for i in array.matrix[r] if numpy.isfinite(i)]
matrix_max = numpy.max(matrix_dist)
matrix_min = numpy.min(matrix_dist)
matrix_avg = matrix_min + ((matrix_max - matrix_min) / 2)
# Creates a profile face that will represent node's profile as a
# heatmap
profileFace = ProfileFace(1., 0., 0.5, 1000, 14, "heatmap", colorscheme=1)
nameFace = AttrFace("name", fsize=8)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"] = 0
add_face_to_node(nameFace, node, 1, aligned=True)
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
t.render("test.svg", tree_style=ts)
'''
f.close()
t_str = nkTree[0]
t = ClusterTree(t_str, data_mat)
ts = TreeStyle()
ts.margin_left = 20
ts.margin_right = 20
ts.margin_top = 20
ts.margin_bottom = 10
ts.scale = 2
ts.min_leaf_separation = 0
ts.branch_vertical_margin = 0
ts.show_leaf_name = True
ts.show_branch_length = False
ts.show_branch_support = True
setup_heatmap(t,
ts,
header,
center_value=4.5,
color_up=0.9,
color_down=0.56,
color_center="white")
t.render(file_name=in_path + "/heatmap.pdf", tree_style=ts)
newick += ';'
t = Tree(newick, format=1)
ct = ClusterTree(t.write(), text_array=matrix)
addColors(ct)
# nodes are linked to the array table
array = ct.arraytable
# Calculates some stats on the matrix. Needed to establish the color gradients.
matrix_dist = [i for r in xrange(len(array.matrix))for i in array.matrix[r] if np.isfinite(i)]
matrix_max = np.max(matrix_dist)
matrix_min = np.min(matrix_dist)
matrix_avg = (matrix_max+matrix_min)/2
# Creates a profile face that will represent node's profile as a heatmap
profileFace = ProfileFace(matrix_max, matrix_min, matrix_avg, 200, 14, "heatmap",colorscheme=3)
# Creates my own layout function that uses previous faces
def mylayout(node):
# If node is a leaf
if node.is_leaf():
# And a line profile
add_face_to_node(profileFace, node, 0, aligned=True)
node.img_style["size"]=2
# Use my layout to visualize the tree
ts = TreeStyle()
ts.layout_fn = mylayout
# ct.show(tree_style=ts)
t.write(format=9, outfile="output/newick/"+param+".nw")
ct.render('output/pngs/'+param+'.png',tree_style=ts)
#print t
